Analysis of the Transcriptome of the Infective Stage of the Beet Cyst Nematode, H. schachtii.

John Fosu-Nyarko,Reetinder Gill,Fareeha Naz,Paul Nicol,Michael G K Jones

doi:10.1371/journal.pone.0147511

Abstract

The beet cyst nematode, Heterodera schachtii, is a major root pest that significantly impacts the yield of sugar beet, brassicas and related species. There has been limited molecular characterisation of this important plant pathogen: to identify target genes for its control the transcriptome of the pre-parasitic J2 stage of H. schachtii was sequenced using Roche GS FLX. Ninety seven percent of reads (i.e., 387,668) with an average PHRED score > 22 were assembled with CAP3 and CLC Genomics Workbench into 37,345 and 47,263 contigs, respectively. The transcripts were annotated by comparing with gene and genomic sequences of other nematodes and annotated proteins on public databases. The annotated transcripts were much more similar to sequences of Heterodera glycines than to those of Globodera pallida and root knot nematodes (Meloidogyne spp.). Analysis of these transcripts showed that a subset of 2,918 transcripts was common to free-living and plant parasitic nematodes suggesting that this subset is involved in general nematode metabolism and development. A set of 148 contigs and 183 singletons encoding putative homologues of effectors previously characterised for plant parasitic nematodes were also identified: these are known to be important for parasitism of host plants during migration through tissues or feeding from cells or are thought to be involved in evasion or modulation of host defences. In addition, the presence of sequences from a nematode virus is suggested. The sequencing and annotation of this transcriptome significantly adds to the genetic data available for H. schachtii, and identifies genes primed to undertake required roles in the critical pre-parasitic and early post-parasitic J2 stages. These data provide new information for identifying potential gene targets for future protection of susceptible crops against H. schachtii.

Highlights

The beet cyst nematode, H. schachtii, is a sedentary endoparasitic plant nematode present in temperate and mediterranean regions
The total length of the CAP3 and CLC contigs were 35.4% and 19.7%, respectively, of the entire length of all reads of the transcriptome more reads were assembled by the CLC genomics workbench
The J2 stage of a cyst nematode is often viewed as the most important stage in its life cycle because this life stage must be able to move through soil to locate a host root, enter and migrate within it while evading or suppressing the host immune responses, to a site where it initiates the formation of a syncytium

Summary

Introduction

The beet cyst nematode, H. schachtii, is a sedentary endoparasitic plant nematode present in temperate and mediterranean regions. Pre-parasitic cyst nematode stage 2 juveniles (J2s) moult from J1s that develop from eggs within the cysts, and migrate to host plants (Fig 1). They enter root cells using their hollow mouth stylet, aided by secretions produced from gland cells that include cell wall-modifying enzymes such as cellulases and pectinases, and migrate intracellularly, responding to positional gradients in the root [7,8,9]. We report the sequencing of the transcriptome of the infective J2 stage of H. schachtii prior to root entry, and annotation of transcripts using sequences of both free-living and parasitic nematodes, and conserved or core eukaryotic genes. Many of the identified genes need further functional characterisation, it provides a set of sequences that could be used to exploit gene-based strategies such as RNA interference, to develop new strategies for control of this economically important nematode

Ethics Statement

Results

Discussion